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. 2023 Aug 1;39(8):btad492.
doi: 10.1093/bioinformatics/btad492.

NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis

Anna Wierczeiko  1 , Stefan Pastore  2 , Stefan Mündnich  2 , Anne M Busch  1 , Vincent Dietrich  1 , Mark Helm  2 , Tamer Butto  2 , Susanne Gerber  1
Affiliations

NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis

Anna Wierczeiko et al. Bioinformatics. .

Abstract

Summary: Oxford Nanopore Technologies' (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge. Here, we introduce NanopoReaTA, a user-friendly real-time analysis toolbox for RNA-sequencing data from ONT. Sequencing results from a running or finished experiment are processed through an R Shiny-based graphical user interface with an integrated Nextflow pipeline for whole transcriptome or gene-specific analyses. NanopoReaTA provides visual snapshots of a sequencing run in progress, thus enabling interactive sequencing and rapid decision making that could also be applied to clinical cases.

Availability and implementation: Github https://github.com/AnWiercze/NanopoReaTA; Zenodo https://doi.org/10.5281/zenodo.8099825.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
NanopoReaTA workflow visualized as a graphical sketch. (A) Sequencing start; (B) Configuration of settings in NanopoReaTA’s UI; (C) Preprocessing pipeline by Nextflow; (D) Transcriptional analysis and (E) visualization of results in NanopoReaTA’s UI. Detailed information on the individual modules is given in the Supplementary Information, as well as in the user manual on the GitHub repository: https://github.com/AnWiercze/NanopoReaTA.
See this image and copyright information in PMC

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